I am not a doctor, but have had many cystoscopies performed on me in recent years to check for bladder cancer recurrence. I get a a little squirt of lidocaine
in the urethra
as a numbing agent; I thought it was standard practice. Also,most every urologist today uses a flexible cystoscope. If your father's doctor still had the old-fashioned rigid kind, I hear it could be uncomfortable.
Personally, I find the procedure a minor, but necessary, discomfort.